MRG: Add support for data from NIRx Aurora 2021.9 software

doc/changes/latest.inc

@@ -191,6 +191,8 @@ Enhancements
 
 - Add :func:`mne.preprocessing.ieeg.project_sensors_onto_brain` to project ECoG sensors onto the pial surface to compensate for brain shift (:gh:`9800` by `Alex Rockhill`_)
 
+- Add support for data acquired with NIRx devices using Aurora software version 2021.9 (:gh:`9800` by `Robert Luke`_, and `Eric Larson`_)
+
 - All functions for reading and writing files should now automatically handle ``~`` (the tilde character) and expand it to the user's home directory. Should you come across any function that doesn't do it, please do let us know! (:gh:`9613` by `Richard Höchenberger`_)
 
 - All functions accepting a FreeSurfer subjects directory via a ``subjects_dir`` parameter can now consume :py:class:`pathlib.Path` objects too (used to be only strings) (:gh:`9613` by `Richard Höchenberger`_)

mne/datasets/config.py

@@ -87,7 +87,7 @@
 # respective repos, and make a new release of the dataset on GitHub. Then
 # update the checksum in the MNE_DATASETS dict below, and change version
 # here:                  ↓↓↓↓↓         ↓↓↓
-RELEASES = dict(testing='0.123', misc='0.23')
+RELEASES = dict(testing='0.125', misc='0.23')
 TESTING_VERSIONED = f'mne-testing-data-{RELEASES["testing"]}'
 MISC_VERSIONED = f'mne-misc-data-{RELEASES["misc"]}'
 
@@ -307,7 +307,7 @@
 
 MNE_DATASETS['testing'] = dict(
     archive_name=f'{TESTING_VERSIONED}.tar.gz',  # 'mne-testing-data',
-    hash='md5:db07710c0b94476f954f60926685b5b7',
+    hash='md5:0871ae325805a9cd2cdfb2fc74327abb',
     url=('https://codeload.github.com/mne-tools/mne-testing-data/'
          f'tar.gz/{RELEASES["testing"]}'),
     folder_name='MNE-testing-data',

mne/io/nirx/nirx.py

@@ -159,7 +159,8 @@ def __init__(self, fname, saturated, preload=False, verbose=None):
         # Check that the file format version is supported
         if is_aurora:
             # We may need to ease this requirement back
-            if hdr['GeneralInfo']['Version'] not in ['2021.4.0-34-ge9fdbbc8']:
+            if hdr['GeneralInfo']['Version'] not in ['2021.4.0-34-ge9fdbbc8',
+                                                     '2021.9.0-5-g3eb32851']:
                 warn("MNE has not been tested with Aurora version "
                      f"{hdr['GeneralInfo']['Version']}")
         else:
@@ -185,7 +186,8 @@ def __init__(self, fname, saturated, preload=False, verbose=None):
         meas_date = None
         # Several formats have been observed so we try each in turn
         for dt_code in ['"%a, %b %d, %Y""%H:%M:%S.%f"',
-                        '"%a, %d %b %Y""%H:%M:%S.%f"']:
+                        '"%a, %d %b %Y""%H:%M:%S.%f"',
+                        '%Y-%m-%d %H:%M:%S.%f']:
             try:
                 meas_date = dt.datetime.strptime(datetime_str, dt_code)
                 meas_date = meas_date.replace(tzinfo=dt.timezone.utc)
@@ -271,9 +273,10 @@ def __init__(self, fname, saturated, preload=False, verbose=None):
             subject_info['sex'] = FIFF.FIFFV_SUBJ_SEX_FEMALE
         else:
             subject_info['sex'] = FIFF.FIFFV_SUBJ_SEX_UNKNOWN
-        subject_info['birthday'] = (meas_date.year - int(inf['age']),
-                                    meas_date.month,
-                                    meas_date.day)
+        if inf['age'] != '':
+            subject_info['birthday'] = (meas_date.year - int(inf['age']),
+                                        meas_date.month,
+                                        meas_date.day)
 
         # Read information about probe/montage/optodes
         # A word on terminology used here:

mne/io/nirx/tests/test_nirx.py

@@ -52,14 +52,24 @@
 nirsport2_snirf = op.join(data_path(download=False), 'SNIRF', 'NIRx',
                           'NIRSport2', '1.0.3', '2021-05-05_001.snirf')
 
+nirsport2_2021_9 = op.join(data_path(download=False), 'NIRx', 'nirsport_v2',
+                           'aurora_2021_9')
+snirf_nirsport2_20219 = op.join(data_path(download=False),
+                                'SNIRF', 'NIRx', 'NIRSport2', '2021.9',
+                                '2021-10-01_002.snirf')
+
 
 @requires_h5py
 @requires_testing_data
 @pytest.mark.filterwarnings('ignore:.*Extraction of measurement.*:')
-def test_nirsport_v2_matches_snirf():
+@pytest.mark.parametrize('fname_nirx, fname_snirf', (
+    [nirsport2, nirsport2_snirf],
+    [nirsport2_2021_9, snirf_nirsport2_20219],
+))
+def test_nirsport_v2_matches_snirf(fname_nirx, fname_snirf):
     """Test NIRSport2 raw files return same data as snirf."""
-    raw = read_raw_nirx(nirsport2, preload=True)
-    raw_snirf = read_raw_snirf(nirsport2_snirf, preload=True)
+    raw = read_raw_nirx(fname_nirx, preload=True)
+    raw_snirf = read_raw_snirf(fname_snirf, preload=True)
 
     assert_allclose(raw._data, raw_snirf._data)
 
@@ -559,7 +569,8 @@ def test_nirx_15_0():
 @pytest.mark.parametrize('fname, boundary_decimal', (
     [fname_nirx_15_2_short, 1],
     [fname_nirx_15_2, 0],
-    [fname_nirx_15_0, 0]
+    [fname_nirx_15_2, 0],
+    [nirsport2_2021_9, 0]
 ))
 def test_nirx_standard(fname, boundary_decimal):
     """Test standard operations."""

mne/io/snirf/tests/test_snirf.py

@@ -36,6 +36,11 @@
 nirx_nirsport2_103_2 = op.join(data_path(download=False),
                                'SNIRF', 'NIRx', 'NIRSport2', '1.0.3',
                                '2021-05-05_001.snirf')
+snirf_nirsport2_20219 = op.join(data_path(download=False),
+                                'SNIRF', 'NIRx', 'NIRSport2', '2021.9',
+                                '2021-10-01_002.snirf')
+nirx_nirsport2_20219 = op.join(data_path(download=False), 'NIRx',
+                               'nirsport_v2', 'aurora_2021_9')
 
 
 @requires_h5py
@@ -45,7 +50,8 @@
                                     nirx_nirsport2_103,
                                     sfnirs_homer_103_153,
                                     nirx_nirsport2_103,
-                                    nirx_nirsport2_103_2]))
+                                    nirx_nirsport2_103_2,
+                                    snirf_nirsport2_20219]))
 def test_basic_reading_and_min_process(fname):
     """Test reading SNIRF files and minimum typical processing."""
     raw = read_raw_snirf(fname, preload=True)
@@ -284,10 +290,18 @@ def test_snirf_nirsport2_w_positions():
 
 @requires_testing_data
 @requires_h5py
-def test_snirf_standard():
+@pytest.mark.parametrize('fname, boundary_decimal, test_scaling, test_rank', (
+    [sfnirs_homer_103_wShort, 0, True, True],
+    [nirx_nirsport2_103, 0, True, False],  # strange rank behavior
+    [nirx_nirsport2_103_2, 0, False, True],  # weirdly small values
+    [snirf_nirsport2_20219, 0, True, True],
+))
+def test_snirf_standard(fname, boundary_decimal, test_scaling, test_rank):
     """Test standard operations."""
-    _test_raw_reader(read_raw_snirf, fname=sfnirs_homer_103_wShort,
-                     boundary_decimal=0)  # low fs
+    _test_raw_reader(read_raw_snirf, fname=fname,
+                     boundary_decimal=boundary_decimal,
+                     test_scaling=test_scaling,
+                     test_rank=test_rank)  # low fs
 
 
 @requires_testing_data

mne/io/tests/test_raw.py

@@ -200,15 +200,18 @@ def _test_raw_reader(reader, test_preloading=True, test_kwargs=True,
         # ranks should all be reduced by 1
         if test_rank == 'less':
             cmp = np.less
-        else:
+        elif test_rank is False:
+            cmp = None
+        else:  # anything else is like True or 'equal'
+            assert test_rank is True or test_rank == 'equal', test_rank
             cmp = np.equal
         rank_load_apply_get = np.linalg.matrix_rank(data_load_apply_get)
         rank_apply_get = np.linalg.matrix_rank(data_apply_get)
         rank_apply_load_get = np.linalg.matrix_rank(data_apply_load_get)
-        rank_apply_load_get = np.linalg.matrix_rank(data_apply_load_get)
-        assert cmp(rank_load_apply_get, len(col_names) - 1)
-        assert cmp(rank_apply_get, len(col_names) - 1)
-        assert cmp(rank_apply_load_get, len(col_names) - 1)
+        if cmp is not None:
+            assert cmp(rank_load_apply_get, len(col_names) - 1)
+            assert cmp(rank_apply_get, len(col_names) - 1)
+            assert cmp(rank_apply_load_get, len(col_names) - 1)
         # and they should all match
         t_kw = dict(
             atol=atol, err_msg='before != after, likely _mult_cal_one prob')
@@ -280,7 +283,7 @@ def _test_raw_reader(reader, test_preloading=True, test_kwargs=True,
     assert set(raw.info.keys()) == set(raw3.info.keys())
     assert_allclose(raw3[0:20][0], full_data[0:20], rtol=1e-6,
                     atol=1e-20)  # atol is very small but > 0
-    assert_array_almost_equal(raw.times, raw3.times)
+    assert_allclose(raw.times, raw3.times, atol=1e-6, rtol=1e-6)
 
     assert not math.isnan(raw3.info['highpass'])
     assert not math.isnan(raw3.info['lowpass'])